Incidental Mutation 'R4648:Khdc3'
ID 350494
Institutional Source Beutler Lab
Gene Symbol Khdc3
Ensembl Gene ENSMUSG00000092622
Gene Name KH domain containing 3, subcortical maternal complex member
Synonyms FILIA, ecat1, 2410004A20Rik
MMRRC Submission 041909-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.094) question?
Stock # R4648 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 73009118-73011720 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 73009868 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 26 (E26G)
Ref Sequence ENSEMBL: ENSMUSP00000133915 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034722] [ENSMUST00000034737] [ENSMUST00000167514] [ENSMUST00000172578] [ENSMUST00000173734] [ENSMUST00000174203] [ENSMUST00000184146]
AlphaFold Q9CWU5
Predicted Effect probably benign
Transcript: ENSMUST00000034722
SMART Domains Protein: ENSMUSP00000034722
Gene: ENSMUSG00000032202

RAB 10 184 9.9e-92 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000034737
AA Change: E26G

PolyPhen 2 Score 0.806 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000034737
Gene: ENSMUSG00000092622
AA Change: E26G

Pfam:MOEP19 28 113 4.5e-34 PFAM
internal_repeat_1 117 217 6.81e-11 PROSPERO
internal_repeat_1 218 316 6.81e-11 PROSPERO
internal_repeat_2 275 397 3.62e-8 PROSPERO
Predicted Effect possibly damaging
Transcript: ENSMUST00000167514
AA Change: E26G

PolyPhen 2 Score 0.806 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000132527
Gene: ENSMUSG00000092622
AA Change: E26G

internal_repeat_1 117 212 2.21e-8 PROSPERO
internal_repeat_1 207 356 2.21e-8 PROSPERO
Predicted Effect possibly damaging
Transcript: ENSMUST00000172578
AA Change: E26G

PolyPhen 2 Score 0.719 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000133850
Gene: ENSMUSG00000092622
AA Change: E26G

PDB:3V69|B 1 75 4e-49 PDB
Predicted Effect possibly damaging
Transcript: ENSMUST00000173734
AA Change: E26G

PolyPhen 2 Score 0.806 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000133915
Gene: ENSMUSG00000092622
AA Change: E26G

internal_repeat_2 116 194 1.27e-8 PROSPERO
internal_repeat_1 117 231 1.6e-13 PROSPERO
internal_repeat_1 231 341 1.6e-13 PROSPERO
internal_repeat_2 267 344 1.27e-8 PROSPERO
Predicted Effect unknown
Transcript: ENSMUST00000174203
AA Change: E26G
SMART Domains Protein: ENSMUSP00000134473
Gene: ENSMUSG00000092310
AA Change: E26G

internal_repeat_1 116 173 5.47e-9 PROSPERO
internal_repeat_1 177 233 5.47e-9 PROSPERO
Predicted Effect probably benign
Transcript: ENSMUST00000184146
SMART Domains Protein: ENSMUSP00000139310
Gene: ENSMUSG00000032202

RAB 10 184 9.9e-92 SMART
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the KHDC1 family, members of which contain an atypical KH domain that may not bind RNA like canonical KH domains. This gene is specifically expressed in the oocytes, and recent studies suggest that it may function as a regulator of genomic imprinting in the oocyte. Mutations in this gene are associated with recurrent biparental complete hydatidiform mole. [provided by RefSeq, Dec 2011]
PHENOTYPE: Homozygous null mice display a maternal effect defect in embryogenesis with delayed embryonic development and spindle abnormalities resulting in decreased litter sizes for homozygous females. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 85 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700031F05Rik G T X: 101,904,515 (GRCm39) N132K possibly damaging Het
2010315B03Rik T A 9: 124,056,228 (GRCm39) Y232F probably benign Het
2310079G19Rik T C 16: 88,424,255 (GRCm39) S79G probably benign Het
4930568D16Rik T A 2: 35,244,458 (GRCm39) Y298F probably damaging Het
Alpk2 A G 18: 65,482,953 (GRCm39) F352L probably damaging Het
Angpt1 T A 15: 42,539,580 (GRCm39) Y93F probably benign Het
Ankrd33b T C 15: 31,325,170 (GRCm39) *129W probably null Het
Atp5pf T C 16: 84,625,343 (GRCm39) M87V probably benign Het
Atp8b3 A G 10: 80,361,457 (GRCm39) S822P possibly damaging Het
Bbs10 A G 10: 111,136,995 (GRCm39) K703E probably benign Het
Bbs2 A T 8: 94,807,507 (GRCm39) V429E probably damaging Het
Bccip C T 7: 133,316,628 (GRCm39) L83F probably damaging Het
Brd9 G A 13: 74,088,895 (GRCm39) V198I probably benign Het
C1galt1c1 A T X: 37,720,349 (GRCm39) S216T probably benign Het
Calhm1 A G 19: 47,132,240 (GRCm39) L125P probably damaging Het
Ccdc110 A T 8: 46,395,705 (GRCm39) Q532L possibly damaging Het
Cdh19 G A 1: 110,852,907 (GRCm39) L343F probably benign Het
Cep350 A G 1: 155,778,344 (GRCm39) S1653P possibly damaging Het
Cmtm4 A G 8: 105,082,952 (GRCm39) I135T possibly damaging Het
Cmya5 A G 13: 93,230,336 (GRCm39) L1584P possibly damaging Het
Crocc2 G A 1: 93,096,516 (GRCm39) V24M possibly damaging Het
Crp A G 1: 172,525,704 (GRCm39) M1V probably null Het
Csmd1 G A 8: 16,048,788 (GRCm39) Q2305* probably null Het
Cyp2c38 T A 19: 39,449,132 (GRCm39) I74F probably benign Het
Dab1 C T 4: 104,588,948 (GRCm39) A524V probably benign Het
Dcaf1 A T 9: 106,742,876 (GRCm39) probably benign Het
Dhx16 C G 17: 36,196,527 (GRCm39) A565G probably benign Het
Dock7 C A 4: 98,857,881 (GRCm39) E1448* probably null Het
Dpf2 C T 19: 5,957,109 (GRCm39) R38H probably damaging Het
E030030I06Rik T A 10: 22,024,744 (GRCm39) R56S unknown Het
Etnk1 A G 6: 143,141,000 (GRCm39) Y248C probably damaging Het
Ext1 A G 15: 52,953,383 (GRCm39) S494P possibly damaging Het
Gk2 T C 5: 97,603,579 (GRCm39) S420G probably benign Het
Gm26596 T C 10: 112,765,064 (GRCm39) probably benign Het
Gm5414 G T 15: 101,536,543 (GRCm39) N27K possibly damaging Het
Gskip A G 12: 105,664,988 (GRCm39) D9G probably benign Het
H2-K2 T A 17: 34,194,989 (GRCm39) noncoding transcript Het
Hk1 T G 10: 62,140,558 (GRCm39) S105R probably benign Het
Hmg20b T A 10: 81,184,416 (GRCm39) Q129L probably damaging Het
Idnk A G 13: 58,310,683 (GRCm39) D67G probably benign Het
Igfbp5 G T 1: 72,903,222 (GRCm39) H118N probably benign Het
Irf4 A T 13: 30,947,580 (GRCm39) Y427F probably benign Het
Kif7 T C 7: 79,358,939 (GRCm39) D512G probably damaging Het
Lamb3 T A 1: 193,013,665 (GRCm39) I513N probably damaging Het
Lipo3 A G 19: 33,760,860 (GRCm39) L174P probably damaging Het
Lnx1 C T 5: 74,771,457 (GRCm39) V350I probably benign Het
Map3k21 A G 8: 126,668,850 (GRCm39) D812G probably benign Het
Mast2 G T 4: 116,172,036 (GRCm39) Y637* probably null Het
Matn2 T C 15: 34,428,679 (GRCm39) I681T probably damaging Het
Med18 A T 4: 132,190,274 (GRCm39) V37D possibly damaging Het
Mip T A 10: 128,062,922 (GRCm39) H122Q probably benign Het
Mmp13 A T 9: 7,274,233 (GRCm39) D180V probably damaging Het
Mpg C A 11: 32,180,034 (GRCm39) C187* probably null Het
Mtmr14 A G 6: 113,237,567 (GRCm39) E256G probably benign Het
Myo7b C T 18: 32,100,178 (GRCm39) probably null Het
Nhsl3 G T 4: 129,115,733 (GRCm39) T977K probably benign Het
Nmt1 T A 11: 102,954,743 (GRCm39) V425D probably damaging Het
Nynrin T A 14: 56,110,351 (GRCm39) Y1819* probably null Het
Or10ak16 A G 4: 118,751,147 (GRCm39) N289S possibly damaging Het
Or4c107 T A 2: 88,789,556 (GRCm39) F249I probably damaging Het
Or5i1 T C 2: 87,613,565 (GRCm39) V227A possibly damaging Het
Otof T C 5: 30,540,914 (GRCm39) E875G possibly damaging Het
Paqr3 T A 5: 97,256,069 (GRCm39) R102* probably null Het
Phc1 T C 6: 122,298,872 (GRCm39) I699V possibly damaging Het
Prkdc T G 16: 15,634,638 (GRCm39) D3594E probably benign Het
Pstpip1 A T 9: 56,032,502 (GRCm39) D246V probably damaging Het
Rbm46 A T 3: 82,771,765 (GRCm39) D283E probably benign Het
Ror2 A T 13: 53,439,536 (GRCm39) C9* probably null Het
Setd1b C T 5: 123,286,175 (GRCm39) A407V unknown Het
Slc26a4 T G 12: 31,590,525 (GRCm39) D376A possibly damaging Het
Smarcad1 A G 6: 65,044,073 (GRCm39) E215G probably benign Het
Spag16 G A 1: 69,866,194 (GRCm39) R11Q probably null Het
Sult1d1 T A 5: 87,713,954 (GRCm39) Q30L probably benign Het
Tbc1d5 A G 17: 51,043,251 (GRCm39) C746R probably benign Het
Tdh A G 14: 63,731,205 (GRCm39) L323P possibly damaging Het
Tet2 A T 3: 133,193,843 (GRCm39) M197K probably benign Het
Tnn T C 1: 159,973,612 (GRCm39) M252V probably benign Het
Trdn G T 10: 33,071,977 (GRCm39) E215* probably null Het
Trem1 G A 17: 48,551,590 (GRCm39) V84I probably benign Het
Tspan5 T C 3: 138,604,076 (GRCm39) F154L probably damaging Het
Usp45 A G 4: 21,825,044 (GRCm39) R647G probably benign Het
Usp50 T A 2: 126,619,953 (GRCm39) I120F probably damaging Het
Vil1 T C 1: 74,471,457 (GRCm39) M746T probably benign Het
Washc4 T A 10: 83,410,407 (GRCm39) M665K possibly damaging Het
Zfp750 T C 11: 121,402,706 (GRCm39) T681A probably benign Het
Other mutations in Khdc3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02987:Khdc3 APN 9 73,009,948 (GRCm39) missense possibly damaging 0.56
R1487:Khdc3 UTSW 9 73,009,846 (GRCm39) missense probably benign 0.19
R1523:Khdc3 UTSW 9 73,010,773 (GRCm39) missense possibly damaging 0.53
R1545:Khdc3 UTSW 9 73,010,942 (GRCm39) missense probably benign 0.05
R1951:Khdc3 UTSW 9 73,010,519 (GRCm39) missense possibly damaging 0.48
R2935:Khdc3 UTSW 9 73,010,987 (GRCm39) missense possibly damaging 0.92
R3076:Khdc3 UTSW 9 73,010,212 (GRCm39) missense probably damaging 1.00
R3880:Khdc3 UTSW 9 73,010,872 (GRCm39) missense possibly damaging 0.73
R3899:Khdc3 UTSW 9 73,011,628 (GRCm39) intron probably benign
R3900:Khdc3 UTSW 9 73,011,628 (GRCm39) intron probably benign
R4224:Khdc3 UTSW 9 73,010,153 (GRCm39) missense possibly damaging 0.92
R4412:Khdc3 UTSW 9 73,010,156 (GRCm39) missense possibly damaging 0.93
R4529:Khdc3 UTSW 9 73,011,301 (GRCm39) missense possibly damaging 0.83
R4647:Khdc3 UTSW 9 73,009,868 (GRCm39) missense possibly damaging 0.81
R5153:Khdc3 UTSW 9 73,010,720 (GRCm39) missense probably benign 0.18
R5261:Khdc3 UTSW 9 73,010,768 (GRCm39) missense possibly damaging 0.92
R8362:Khdc3 UTSW 9 73,010,848 (GRCm39) missense possibly damaging 0.96
X0024:Khdc3 UTSW 9 73,011,206 (GRCm39) missense probably benign 0.01
X0026:Khdc3 UTSW 9 73,010,265 (GRCm39) missense possibly damaging 0.95
X0066:Khdc3 UTSW 9 73,011,463 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2015-10-08